SUPPLEMENTARY MATERIALS Supplementary method - Deep sequencing Regarding R105, a mosaic variant in MECP2 exon 1 (NM_001110792.1: c.31G>T, p.Gly11*) was confirmed by targeted amplicon sequencing (TAS) using DNA derived from peripheral blood leukocytes, saliva, nails, and hair roots of the affected individuals. TAS libraries were prepared using reagents from the SureSelect XT Human All Exon kit (Agilent Technologies), in accordance with the manufacturer’s instructions. The TAS library was run on a MiSeq sequencer (Illumina) with 150-bp paired-end reads. Alignment, recalibration, and variant calling were performed as previously described for WES without PCR deduplication. Allele frequency was calculated based on manual read counts in bam files using the Integrative Genomics Viewer (IGV, http://www.broadinstitute.org/igv/). ID Analysis status Gene Phenotype group (reason suspected as RTT‐ A period of Main criteria Exclusion criteria for typical RTT Supportive criteria for atypical RTT like for group 3) regression followed 1. Partial or complete 2. Partial or complete 3. Gait abnormalities: 4. Stereotypic hand 1. Brain injury secondary to trauma (peri‐ or 1. Breathing disturbances when awake 1. typical RTT by recovery or loss of acquired loss of acquired Impaired (dyspraxic) movements such as postnatally), neurometabolic disease, or severe 2. Bruxism when awake 2. atypical RTT stabilization purposeful hand spoken language or absence of ability. hand infection that causes neurological problems 3. Impaired sleep pattern 3. RTT‐like features skills. wringing/squeezing, 2. Grossly abnormal psychomotor development in first 4. Abnormal muscle tone clapping/tapping, 6 months of life 5. Peripheral vasomotor disturbances mouthing and 6. Scoliosis/kyphosis washing/rubbing 7. Growth retardation automatisms 8. Small cold hands and feet 9. Inappropriate laughing/screaming spells 10. Diminished response to pain 11. Intense eye communication "eye pointing" R002 SNV_identified CACNA1G 3, autistic behavor with stereotypic No No No Yes Yes 1,2,4,5,6,7,10,11 movements and gait abnormalities R006 SNV_identified SHANK3 1, typical RTT Yes Yes Yes Yes Yes 2,3,4,5,6,7,8,10,11 R008 CNV_identified STXBP1_deletion 3, autistic spectrum disorder with hypotonia No No No Yes Yes 1,2,3,4,6,7,8,10 and intellectual disability R016 VUS TCF4 3, stereotypic movements No No No Yes Yes Brain injury perinatally 2,3,4,6,7,8 AMU3 SNV_identified SCN8A 2, atypical RTT Yes Yes No Yes Yes 2,3,4,6,9, AMU4 SNV_identified PDHA1 3, clinical atypical RTT without metabolic Yes No No Yes Yes 2,4,6,7,8,10 disease exclusion AMU5 SNV_identified CDKL5 2, atypical RTT Yes Yes No Yes Yes 2,3,4,7,8,9 SN01 Candidate ATP6V0A1 2, atypical RTT Yes Yes No Yes Yes 1,3,4,6,7,9 SN04 SNV_identified MAST1 2, atypical RTT Yes No No Yes Yes 2,3,4,7,9,10 SN05 MECP2_CNV MECP2 1, typical RTT Yes Yes Yes Yes Yes 3,4,7,9, SN06 SNV_identified PPT1 2, atypical RTT Yes Yes Yes Yes Yes 3,4,9, SN07 VUS UBE3A 2, atypical RTT Yes Yes No Yes No 2,3,4,9, SN08 SNV_identified FOXG1 2, atypical RTT Yes Yes No Yes Yes 3,4,7,9, SN12 CNV_identified MEF2C_deletion 2, atypical RTT Yes Yes No Yes Yes 2,3,4,6,7 SN14 MECP2_CNV MECP2 1, typical RTT Yes Yes Yes Yes Yes 1,2,3,4,6 SN15 SNV_identified STXBP1 2, atypical RTT Yes Yes No Yes Yes Pathologically diagnosed atypical Wilson disease 2,4,9,11 (biallelic variants in ATP7B were not found.) SN16 VUS PCDH19 2, atypical RTT Yes Yes Yes Yes Yes 4,9 R039 SNV_identified UBE3A 3, suspected of RTT and angelman syndrome No No No Yes No 3,4,7,9 with epilepsy R040 MECP2_CNV MECP2 1, typical RTT Yes Yes Yes Yes Yes N.D. R046 SNV_identified UBE3A 3, developmental delay with scoliosis No No No Yes No 6 R047 SNV_identified HDAC8 2, atypical RTT Yes Yes Yes Yes Yes 1,2,3,4,5,7,8,9,10,11 R048 VUS GRIN2B 1, typical RTT Yes Yes Yes Yes Yes 6 R049 SNV_identified TCF4 2, atypical RTT No No Yes Yes Yes 6 R050 SNV_identified STXBP1 3, developmental delay with walk disability No No No Yes No N.D. R053 SNV_identified NR2F1 3, stereotypic movements of hands Yes No No Yes Yes 4 R066 SNV_identified WDR45 1, typical RTT Yes Yes Yes Yes Yes 1,2,4,5,6,7,8,11 R072 SNV_identified SYNGAP1 3, abnormal sleep pattern No No No No No 3 R076 SNV_identified GRIN2B 3, developmental delay with scoliosis, No No No No No 2,6 abnormal sleep pattern R078 CNV_identified 22q13 deletion 3, walk disability and scoliosis No No No Yes No N.D. R082 CNV_identified 2p23 microdeletion 3, autistic spectrum disorder with hypotonia No No No Yes No N.D. and intellectual disability R092 SNV_identified UBE3A 3, autistic spectrum disorder with hypotonia No No No Yes No N.D. and sleep disturbance R093 SNV_identified NALCN 3, female with acquired microcephaly No Yes No Yes Yes 1,2,3,4,7,8, R095 Candidate USP8 2, atypical RTT Yes No No Yes Yes 1,2,3,4,6,7,8,9 R096 Candidate NCOR2 3, microcephalus No No No Yes No N.D. R097 SNV_identified SCN2A 1, typical RTT Yes Yes Yes Yes Yes N.D. R104 SNV_identified IQSEC2 1, typical RTT Yes Yes Yes Yes Yes N.D. R105 Mosaic mecp2_e1 2, atypical RTT Yes Yes Yes Yes Yes 1,2,5,8,9,11 R106 SNV_identified STXBP1 2, atypical RTT Yes Yes Yes Yes Yes N.D. R110 SNV_identified IRF2BPL 3, stereotypic movements, autistic feature No No No No Yes Mild psychomotor delay (head control at 5 months, sit 4 alone at 2 years) R112 CNV_identified WDR45_deletion 2, atypical RTT No No No Yes Yes 1,2,7,9 R113 SNV_identified WDR45 3, stereotypic movements No No No Yes Yes N.D. R114 SNV_identified STXBP1 3, stereotypic movements No No No Yes Yes 4 R115 SNV_identified ITPR1 3, autistic feature No No Yes No No 2,4 R120 SNV_identified WDR45 2, atypical RTT No No No Yes Yes Influenza encephalopathy N.D. R122 SNV_identified CUX2 3, stereotypic movements No No No No Yes 1,2,3 R123 SNV_identified FOXG1 3, microcephalus No No No No No N.D. R124 SNV_identified SHANK3 2, atypical RTT No No No Yes Yes N.D. R127 SNV_identified KIF1A 3, autistic behaivor with gait abnormalities No No No Yes Yes Mild developmental delay at infantile 4,5,6,7,8,9,10 R128 SNV_identified WDR45 3, stereotypic movements, microcephalus No No No No Yes 3,4 R129 SNV_identified CACNA1D 3, stereotypic movements with gait No No No Yes Yes N.D. abnormalities R130 SNV_identified CAMK2B 3, stereotypic movements, microcephalus No No No No Yes 3,4,7 R132 Candidate MAST3 3, autistic behavior with gait abnormalities Yes No No Yes No 3,4,9,11 R133 SNV_identified GABRA1 3, autistic behavor, stereotypic movements No Yes Yes Yes Yes Infantile spasms at three month‐of‐age 1,2,3,4,10 R135 SNV_identified SHANK3 3, autistic behavor with gait abnormalities No No No Yes No N.D. R136 SNV_identified COL4A1 3, autistic feature, stereotypic movements No No No No Yes 4 Supplementary table S1. Diagnostic criteria for Rett syndrome (RTT) of 55 patients with variants in known and novel genes Typical and atypical RTT were evaluated based on the main criteria for RTT in this study [2]. Supportive criteria for atypical RTT were partially available. Abbreviations: N.D., no data; SNV, single nucleotide variant; CNV, copy number variation; VUS, variants of uncertain significance. Capture kit Covered regions (%) Patient ID (SureSelect Human All Sequenced base (bp) Mean depth Exon kit version) > 5 reads > 10 reads > 20 reads R002 50Mb 3704090949 110.66 97.2 96.4 94 R004_Patient1 v6 2738293353 81.81 98.1 97.6 95.7 R004_Patient2 v6 2837108719 84.76 98 97.5 95.8 R006 50Mb 4204356545 125.61 97.3 96.6 94.7 R008 v6 2670429622 79.78 98 97.5 95.6 R010_Patient1 v4 3786038604 113.11 95.9 94.5 90.4 R010_Patient2 v4 3695649497 110.41 95.8 94.4 90.4 R0014 v4 4069973828 121.59 96 94.6 91 R0015 v4 3911072574 116.85 95.8 94.4 90.5 R0016 v4 4851694116 144.95 96.1 94.9 91.9 AMU1 v4 2952284454 88.2 95.3 93.1 87 AMU3 v4 2626688060 78.42 94.9 92.2 84.7 AMU4 v4 3817383658 114.05 95.8 94.4 90.3 AMU5 v4 3630014086 108.38 95.5 93.8 89.1 SN01 v4 3933550662 117.52 95.9 94.4 90.6 SN02 v4 4070290908 121.6 95.9 94.5 90.9 SN03 v4 3908355894 116.76 95.9 94.5 90.7 SN04 v4 3813528681 113.93 95.8 94.3 90.3 SN05 v4 3757856048 112.27 95.9 94.4 90.5 SN06 v4 3856444464 115.21 95.9 94.5 90.6 SN07 v4 3174765631 94.85 95.6 93.8 88.7 SN08 v4 3617335584 108.07 95.8 94.2 89.9 SN09 v4 3904330157 116.64 95.9 94.4 90.6 SN11 v4 4031302359 120.44 95.9 94.6 91 SN12 v4 3392802503 101.36 95.7 94 89.3 SN13 v4 4032949334 120.49 95.9 94.6 90.9 SN14 v4 3857364294 115.24 95.9 94.5 90.6 SN15 v4 3629653169 108.44 95.8 94.2 90 SN16 v4 4305871744 128.64 96 94.7 91.3 SN17 v4 3658458674 109.3 95.7 94 89.7 R039_Patient1 v4 4605782320 137.6 96.3 95.3 92.4 R039_Patient2 v4 5736829917 171.39 96.4 95.6 93.5 R040_Patient1 v4 5647781103 168.73 96.5 95.7 93.8 R040_Patient2 v4 6019721174 179.84 96.4 95.6 93.6 R046 v5 4955181217 148.04 96.2 95.1 92.4 R047 v5 4135150133 123.54 96 94.7 91.2 R048 v5 4855006629 145.05 96.1 95 92.2 R049 v5 4336345033 129.55 96 94.7 91.3 R050 v5 4439183407 132.62 96 94.6 91.2 R053 v5 4394326408 131.28 96 94.6 91.2 R066 v5 4717077393 140.93 96.1 95 92 R072 v5 4632252763 138.39 96.2 95.3 93.4 R076 v5 4487942762 134.08 97.4 96.8 95.1 R078 v5 3051793184 91.17 94.2 89.4 79.7 R082 v5 2943981593 87.95 97 95.8 92.3 R091 v5 2630348641 78.58 97.2 96 91.9 R092 v5 2965753471 88.6 97.2 96.3 92.2 R093 v5 2655606406 79.34 97.1 96 93.2 R095 v5 2786061084 83.24 97.3 96.2 92.5 R096 v5 2757762704 82.39 97.1 96 92.3 R097 v5 3352003219 100.14 97.2 96.3 93.5 R104 v6 1952649879 58.34 97.5 96.2 91.8 R105 v6 2820397535 84.26 98 97.4 95.3 R106 v6 2094689063 62.58 97.9 97 93.5 R107 v6 2771793878 82.81 98.1 97.6 95.9 R108 v6 2451296100 73.23 98 97.3 94.7 R110 v6 1955631055